Sequence
atgc intronic sequence ATGC exonic sequence...aatggtgacatataagtgtttttgcatatgctatgctgttttctggtgtgctgcaataatactctatatgatttttcttttttgcacatcactgatgcagAGCATCAAAGGAGGAGGCCATCCTCATCCTTTAAACATTGGTGATTTGTTTTCAGAAGGGTCTCTTAATCCATATGCAGAGGATCCCTATGCATTTGAT
Basic information
species | Glycine max |
transcript | GLYMA13G01840.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G01840.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os04g37960.1 (Oryza sativa), 3'ss of exon 19
aatggtgacatataagtgtttttgcatatgc-tatgctgttttctggtgtgctgcaataatact-ctatatgatttttcttttttgcacatcactgatgcagAGCATCAAAGGAGGAGGCCATCCTCATCCTTTAAACATTGGTGATTTGTTTTCAGAAGGGTCTCTTAATCCATATGCAGAGGATCCCTATGCATTTGAT----
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----attcgatcagagtctatccgaaaacatgcatccagaatattggttttcccagatgcttttgctcaacttttgttaacatttacgcttcttcactctccag-
upper sequence: GLYMA13G01840.1 (Glycine max), 3'ss of exon 17
lower sequence: AT1G22275.1 (Arabidopsis thaliana), 3'ss of exon 17
aatggtgacatataagtgtttttgc--atatgctatgctgttttctggtgtgctgcaataatactctatatgatttttcttttttgcacatcactga-tgcagAGCATCAAAGGAGGAGGCCATCCTCATCCTTTAAACATTGGTGATTTGTTTTCAGAAGGGTCTCTTAATCCATATGCAGAGGATCCCTATGCATTTGAT-
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---tataatgtagaagttttcaggccaagaagttatggatgatgctaggtttctaaaaacatttctgatttaactgcatattattctggtcttttaagcgcagGAAACAGCAATGGCCGATCATCCTCACTCTGCAAATATTGGAGACTTGTTTTCAGAAGGTTCCCTCAACCCATATGCTGATGATCCCTATGCATTTGATT
upper sequence: GLYMA13G01840.1 (Glycine max), 3'ss of exon 17
lower sequence: AT1G22260.1 (Arabidopsis thaliana), 3'ss of exon 17
-----aatggtgacatataagtgtttttgcatatgctatgctgttttctggtgtgctgcaataatactctatatgatttttcttttttgcacatcactgatgcagAGCATCAAAGGAGGAGGCCATCCTCATCCTTTAAACATTGGTGATTTGTTTTCAGAAGGGTCTCTTAATCCATATGCAGAGGATCCCTATGCATTTGAT-
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tccggcacttagaaatgtagaaatttgt-tttaagtcaagaagttatggatgctgctgctaggttctaaaacgtgttctgagttaattgcatatta----tgcagGGCACAGGAATGACGAGTCATGCTCGCTCTGCAAATATTGGAGACTTGTTTTCAGAAGGTTCTCTCAACCCATATGCTGATGATCCCTATGCATTTGATT
upper sequence: GLYMA13G01840.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv18s0001g05600.t01 (Vitis vinifera), 3'ss of exon 17
aatggt--gacatataagtgtttttgcatatgctatgctgttttctggtgtgctgcaataatactctatatgatttttcttttttgcacatcactgatgcagAGCATCAAAGGAGGAGGCCATCCTCATCCTTTAAACATTGGTGATTTGTTTTCAGAAGGGTCTCTTAATCCATATGCAGAGGATCCCTATGCATTTGAT-
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actagttgaatataaaagtgaaccattattctttacagtgcaactatatttatttcctttctgcttatcggagtttgttctatttgta--ttccttgtgcagGAAATTAAGGGAGATAGGCATCTACACCCTTCAAATATAGGCGAGTTATTTTCAGAAGGCTCTCTTAATCCATATGCAGATGATCCTTATGCATTTGATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgtgctgcaataatactctatatgatttttcttttttgcacatcactgatgcagAGCATCAAAGGAGGAGGCCATCCTCATCCTTTAAACATTGGTGATTTGTTTTCAGAAGGGTCTCTTAATCCATATGCAGAGGATCCCTATGCATTTGAT
cactgat putative branch site (score: 3)
aataatactctatatg TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatggtgacatataagtgtttttgcatatgctatgctgttttctggtgtgctgcaataatactctatatgatttttcttttttgcacatcactgatgcagAGCATCAAAGGAGGAGGCCATCCTCATCCTTTAAACATTGGTGATTTGTTTTCAGAAGGGTCTCTTAATCCATATGCAGAGGATCCCTATGCATTTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- tggtgac
- - - - - - - - - - - tgcatat
- - - - - - - - - - - - - - - ctatgct
- - - - - - - - - - - - - - - - - - - - - -tggtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - ctgcaat